Dear all
I have simulated my system 7 different temperature from 300K~500K.Every
time I simulated for 10ns. But when I run the simulation above 500K (I.e
530K/550K/560K) the simulation was crash in NPT equilibrium stage with
following warning.
*step XXX: Water molecule starting at atom can no
Dear gmx-usersI need to create a topology for my designed drug as a ligand to
minimize it in the vacuo in the absence of the protein. But I dont know how can
i convert the DRG.itp file which I obtained from PRODRG site to a .top file . I
searched in the Google and found " Re: minimizing ligand o
Hi,
Parrinello Rahman is not a great choice for the first stages of
equilbration, as suggested at e.g.
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
Your choice of temperature coupling groups is also an anti-pattern, e.g.
http://www.gromacs.org/Documentation/Terminolo
Hello Justin,
I see now why there aren't checkpoint files being produced. I guess I
wanted to checkpoint files, in case the EM didn't converge in n steps, then
I could keep going from that point instead of starting over with >n steps.
Thanks for the response.
Yonatan
On Fri, Jul 7, 2017 at 8:14
Hello,
I have ran an md simulation which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps), and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajecto
Hello,
I have ran an md simulation which has 6 frames (3000 / 500 ie.,
nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps), and now i need to
get the trajectories, but this will be of very huge data (which gives
trajectories of interval of every 0.5 ps)...So how can i get the
trajecto
Hi,
Look at "gmx help trjconv" ;-) The b and e options aren't measured in
frames, and another option is available for selecting frames at different
time intervals.
Mark
On Mon, 10 Jul 2017 06:06 Dilip H N wrote:
> Hello,
> I have ran an md simulation which has 6 frames (3000 / 500 ie.
Hi Justin,
Thanks a lot for the valuable advice.
"A society with free knowledge is better than a society with free food"
On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:
> Hi Justin,
> Thanks a lot for the advice. It looks like I had put one at
Hi,
You can't do that with normal gromacs. But googling may reveal options.
Mark
On Sat, 8 Jul 2017 14:07 Shivangi Agarwal
wrote:
> hello to all
>
> How can i perform PBSA in gromacs
>
>
> Thanks in advance
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.groma
Thank you Justin
Every time your comment helped me.
I should compare two system that are Zn_binding protein and Fe_binding
protein.
So I need force field that satisfies the following conditions.
First, force field contains two metal ion (Fe and Zn)information.
Second, force field contain metal io
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